table of contents
| SIMKAMIN(1) | User Commands | SIMKAMIN(1) |
NAME¶
simkaMin - comparative metagenomics method dedicated to NGS datasets
DESCRIPTION¶
[main options]:¶
- -in
- (1 arg) : input file of datasets. One sample per line: id1: filename1...
- -out
- (1 arg) : output directory for result files (distance matrices) [Default: ./simka_results]
- -seed
- (1 arg) : seed used for random k-mer selection [Default: 100]
- -bin
- (1 arg) : path to simkaMinCore program (to be specified if not in PATH, or not in standard installation directory <simkaDir>/build/bin/simkaMinCore)
[core options]:¶
- -nb-cores
- (1 arg) : number of cores [Default: 0]
- -max-memory
- (1 arg) : max memory (MB) [Default: 8000]
[k-mer options]:¶
- -kmer-size
- (1 arg) : size of a kmer [Default: 21]
- -nb-kmers
- (1 arg) : number of kmers used to compute distances [Default: 1000000]
- -filter
- (0 arg) : filter out k-mer seen one time (potentially erroneous)
[read options]:¶
- -max-reads
- (1 arg) : maximum number of reads per sample to process [Default: 0]
- -min-read-size
- (1 arg) : minimal size a read should have to be kept [Default: 0]
- -min-shannon-index
- (1 arg) : minimal Shannon index a read should have to be kept. Float in [0,2] [Default: 0]
AUTHOR¶
This manpage was written by Shayan Doust for the Debian distribution and can be used for any other usage of the program.
| September 2019 | simkaMin 1.5.1 |